{"id":2445,"date":"2014-07-18T15:53:36","date_gmt":"2014-07-18T19:53:36","guid":{"rendered":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/?page_id=2445"},"modified":"2014-07-21T17:01:25","modified_gmt":"2014-07-21T21:01:25","slug":"bupid-top-down","status":"publish","type":"page","link":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/cpctools\/bupid-top-down\/","title":{"rendered":"BUPID Top-Down"},"content":{"rendered":"<h1 style=\"padding-top: 40px;\">BUPID Top-Down: Software Tools for Analysis of Top-Down MS\/MS Spectra <em>&#8211; Coming Soon!<\/em><\/h1>\n<p class=\"MsoNormal\" style=\"margin-bottom: 0.0001pt; line-height: 200%; text-align: justify;\"><span style=\"font-size: 12.0pt; line-height: 115%; font-family: 'Calibri','sans-serif'; mso-ascii-theme-font: minor-latin; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin; mso-bidi-theme-font: minor-latin; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA;\"><strong>BUPID <\/strong>(Boston University Protein Identifier) <strong>Top-Down <\/strong>is a web-based platform developed at the <strong>Cardiovascular Proteomics Center of Boston University School of Medicine (Boston, MA)<\/strong>. The platform provides the means to analyze top-down MS\/MS spectra obtained with a number of fragmentation methods, including CID, ECD, and ETD. Several software tools are available and may be used in any combination.<\/span><\/p>\n<h3 class=\"MsoNormal\" style=\"padding-top: 20px; margin-bottom: 0.0001pt; line-height: 200%; text-align: justify;\">Tools Available<\/h3>\n<ul>\n<li><span style=\"font-size: 12.0pt; line-height: 115%; font-family: 'Calibri','sans-serif'; mso-ascii-theme-font: minor-latin; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin; mso-bidi-theme-font: minor-latin; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA;\">Deconvolution<\/span><\/li>\n<\/ul>\n<ul>\n<li><span style=\"font-size: 12.0pt; line-height: 115%; font-family: 'Calibri','sans-serif'; mso-ascii-theme-font: minor-latin; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin; mso-bidi-theme-font: minor-latin; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA;\">Protein identification<\/span><\/li>\n<\/ul>\n<ul>\n<li><span style=\"font-size: 12.0pt; line-height: 115%; font-family: 'Calibri','sans-serif'; mso-ascii-theme-font: minor-latin; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin; mso-bidi-theme-font: minor-latin; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA;\">Fragment ion assignment<\/span><\/li>\n<\/ul>\n<ul>\n<li><span style=\"font-size: 12.0pt; line-height: 115%; font-family: 'Calibri','sans-serif'; mso-ascii-theme-font: minor-latin; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin; mso-bidi-theme-font: minor-latin; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA;\">Sequence variant analysis<\/span><\/li>\n<\/ul>\n<ul>\n<li><span style=\"font-size: 12.0pt; line-height: 115%; font-family: 'Calibri','sans-serif'; mso-ascii-theme-font: minor-latin; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin; mso-bidi-theme-font: minor-latin; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA;\">Mass shift analysis<\/span><\/li>\n<\/ul>\n<h3 class=\"MsoNormal\" style=\"padding-top: 20px; margin-bottom: 0.0001pt; line-height: 200%; text-align: justify;\">Input Requirements<\/h3>\n<ul>\n<li><span style=\"font-size: 12.0pt; line-height: 115%; font-family: 'Calibri','sans-serif'; mso-ascii-theme-font: minor-latin; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin; mso-bidi-theme-font: minor-latin; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA;\">Deconvoluted peak list or, for raw data, mzML or mzXML files without compression<br \/>\n<\/span><\/li>\n<\/ul>\n<ul>\n<li><span style=\"font-size: 12.0pt; line-height: 115%; font-family: 'Calibri','sans-serif'; mso-ascii-theme-font: minor-latin; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin; mso-bidi-theme-font: minor-latin; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA;\">Additional information depending on selected tools<br \/>\n<\/span><\/li>\n<\/ul>\n<h3 class=\"MsoNormal\" style=\"padding-top: 20px; margin-bottom: 0.0001pt; line-height: 200%; text-align: justify;\">Output<\/h3>\n<ul>\n<li><span style=\"font-size: 12.0pt; line-height: 115%; font-family: 'Calibri','sans-serif'; mso-ascii-theme-font: minor-latin; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin; mso-bidi-theme-font: minor-latin; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA;\">Raw results in YAML format<\/span><\/li>\n<\/ul>\n<ul>\n<li><span style=\"font-size: 12.0pt; line-height: 115%; font-family: 'Calibri','sans-serif'; mso-ascii-theme-font: minor-latin; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin; mso-bidi-theme-font: minor-latin; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA;\">Built-in visualization tools<\/span><\/li>\n<\/ul>\n<ul>\n<li><span style=\"font-size: 12.0pt; line-height: 115%; font-family: 'Calibri','sans-serif'; mso-ascii-theme-font: minor-latin; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin; mso-bidi-theme-font: minor-latin; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA;\">Convenient download for further analysis (manual; other software)<\/span><\/li>\n<\/ul>\n<h3 class=\"MsoNormal\" style=\"padding-top: 20px; margin-bottom: 0.0001pt; line-height: 200%; text-align: justify;\">Disclaimer<\/h3>\n<p class=\"MsoNormal\" style=\"margin-bottom: 0.0001pt; line-height: 200%; text-align: justify;\"><span style=\"font-size: 12.0pt; line-height: 115%; font-family: 'Calibri','sans-serif'; mso-ascii-theme-font: minor-latin; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin; mso-bidi-theme-font: minor-latin; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA;\">BUPID Top-Down was developed at the <strong>Cardiovascular Proteomics Center of Boston University School of Medicine (Boston, MA)<\/strong>. The software tools are freely available for external testing. We assume no responsibility for their use, and we make no guarantees, whether expressed or implied, about their performance or any other characteristics. We would appreciate acknowledgment of our organization if BUPID Top-Down is used.<\/span><\/p>\n<h3 class=\"MsoNormal\" style=\"padding-top: 20px; margin-bottom: 0.0001pt; line-height: 200%; text-align: justify;\">Publications<\/h3>\n<ul>\n<li style=\"text-align: justify;\"><span style=\"font-size: 12.0pt; line-height: 115%; font-family: 'Calibri','sans-serif'; mso-ascii-theme-font: minor-latin; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin; mso-bidi-theme-font: minor-latin; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA;\"><strong><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/24687996\">Top-down tandem mass spectrometry on RNase A and B using a Qh\/FT-ICR hybrid mass spectrometer<\/a><\/strong><br \/>\nSandrine Bourgoin-Voillard, Nancy Leymarie, and Catherine E. Costello, <strong><em>Proteomics<\/em> 2014<\/strong>, 14(10), 1174-1184.<br \/>\nPMID: 24687996<br \/>\nPMCID: PMC4095805<br \/>\n[PubMed &#8211; in process]<br \/>\n<\/span><\/li>\n<\/ul>\n<ul>\n<li style=\"text-align: justify;\"><span style=\"font-size: 12.0pt; line-height: 115%; font-family: 'Calibri','sans-serif'; mso-ascii-theme-font: minor-latin; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin; mso-bidi-theme-font: minor-latin; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA;\"><strong><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC3098445\">Top-down analysis of small plasma proteins using an LTQ-Orbitrap. Potential for mass spectrometry-based clinical assays for transthyretin and hemoglobin<\/a><\/strong><br \/>\nRoger Theberge, Giuseppe Infusini, Weiwei Tong, Mark E. McComb, and Catherine E. Costello, <strong><em>International Journal of Mass Spectrometry<\/em> 2011<\/strong>, 300(2-3), 130-142.<br \/>\nPMID: 21607198<br \/>\nPMCID: PMC3098445<br \/>\nNIHMSID: NIHMS245609<br \/>\n<\/span><\/li>\n<\/ul>\n<h3 class=\"MsoNormal\" style=\"padding-top: 20px; margin-bottom: 0.0001pt; line-height: 200%; text-align: justify;\">Conference Presentations<\/h3>\n<ul>\n<li style=\"text-align: justify;\"><span style=\"font-size: 12.0pt; line-height: 115%; font-family: 'Calibri','sans-serif'; mso-ascii-theme-font: minor-latin; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin; mso-bidi-theme-font: minor-latin; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA;\"><strong><a href=\"\/cardiovascularproteomics\/files\/2014\/07\/ASMS-2014-BUPID-Heckendorf.pdf\">Automated protein identification and sequencing using top-down MS data<\/a><\/strong><br \/>\nChristian Heckendorf, Roger Theberge, Jean L. Spencer, Catherine E. Costello, and Mark E. McComb, <strong>ASMS 2014<\/strong>, Baltimore, MD.<\/span><\/li>\n<\/ul>\n<ul>\n<li style=\"text-align: justify;\"><span style=\"font-size: 12.0pt; line-height: 115%; font-family: 'Calibri','sans-serif'; mso-ascii-theme-font: minor-latin; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin; mso-bidi-theme-font: minor-latin; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA;\"><strong><a href=\"\/cardiovascularproteomics\/files\/2014\/07\/ASMS-2013-BUPID-Heckendorf.pdf\">Algorithm for identification and sequencing of protein variants using top-down MS data<\/a><\/strong><br \/>\nChristian Heckendorf, Roger Theberge, Jean L. Spencer, Catherine E. Costello, and Mark E. McComb, <strong>ASMS 2013<\/strong>, Minneapolis, MN.<\/span><\/li>\n<\/ul>\n<ul>\n<li style=\"text-align: justify;\"><span style=\"font-size: 12.0pt; line-height: 115%; font-family: 'Calibri','sans-serif'; mso-ascii-theme-font: minor-latin; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin; mso-bidi-theme-font: minor-latin; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA;\"><strong><a href=\"\/cardiovascularproteomics\/files\/2014\/07\/ASMS-2012-BUPID-Heckendorf.pdf\">Development of a web-based top-down protein identification tool<\/a><\/strong><br \/>\nChristian Heckendorf, Roger Theberge, Catherine E. Costello, and Mark E. McComb, <strong>ASMS 2012<\/strong>, Vancouver, BC.<\/span><\/li>\n<\/ul>\n<ul>\n<li style=\"text-align: justify;\"><span style=\"font-size: 12.0pt; line-height: 115%; font-family: 'Calibri','sans-serif'; mso-ascii-theme-font: minor-latin; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin; mso-bidi-theme-font: minor-latin; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA;\"><strong><a href=\"\/cardiovascularproteomics\/files\/2014\/07\/ASMS-2011-BUPID-Heckendorf.pdf\">Development of a web-based top-down data analysis tool<\/a><\/strong><br \/>\nChristian Heckendorf, Roger Theberge, Catherine E. Costello, and Mark E. McComb, <strong>ASMS 2011<\/strong>, Denver, CO.<\/span><\/li>\n<\/ul>\n<ul>\n<li style=\"text-align: justify;\"><span style=\"font-size: 12.0pt; line-height: 115%; font-family: 'Calibri','sans-serif'; mso-ascii-theme-font: minor-latin; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin; mso-bidi-theme-font: minor-latin; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA;\"><strong><a href=\"\/cardiovascularproteomics\/files\/2014\/07\/ASMS-2009-BUPID-Tong.pdf\">BUPID-Top-Down: Database search and assignment of top-down MS-MS data<\/a><\/strong><br \/>\nWeiwei Tong, Roger Theberge, Giuseppe Infusini, David H. Perlman, Catherine E. Costello, and Mark E. McComb, <strong>ASMS 2009<\/strong>, Philadelphia, PA.<\/span><\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>BUPID Top-Down: Software Tools for Analysis of Top-Down MS\/MS Spectra &#8211; Coming Soon! BUPID (Boston University Protein Identifier) Top-Down is a web-based platform developed at the Cardiovascular Proteomics Center of Boston University School of Medicine (Boston, MA). The platform provides the means to analyze top-down MS\/MS spectra obtained with a number of fragmentation methods, including [&hellip;]<\/p>\n","protected":false},"author":7351,"featured_media":0,"parent":558,"menu_order":3,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/wp-json\/wp\/v2\/pages\/2445"}],"collection":[{"href":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/wp-json\/wp\/v2\/users\/7351"}],"replies":[{"embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/wp-json\/wp\/v2\/comments?post=2445"}],"version-history":[{"count":30,"href":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/wp-json\/wp\/v2\/pages\/2445\/revisions"}],"predecessor-version":[{"id":2493,"href":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/wp-json\/wp\/v2\/pages\/2445\/revisions\/2493"}],"up":[{"embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/wp-json\/wp\/v2\/pages\/558"}],"wp:attachment":[{"href":"https:\/\/www.bumc.bu.edu\/cardiovascularproteomics\/wp-json\/wp\/v2\/media?parent=2445"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}